Central control of dynamic gene circuits governs T cell rest and activation

Maya M Arce; Jennifer M Umhoefer; Nadia Arang; Sivakanthan Kasinathan; Jacob W Freimer; Zachary Steinhart; Haolin Shen; Minh T N Pham; Mineto Ota; Anika Wadhera; Rama Dajani; Dmytro Dorovskyi; Yan Yi Chen; Qi Liu; Yuan Zhou; Danielle L Swaney; Kirsten Obernier; Brian R Shy; Julia Carnevale; Ansuman T Satpathy; Nevan J Krogan; Jonathan K Pritchard; Alexander Marson

doi:10.1038/s41586-024-08314-y

Central control of dynamic gene circuits governs T cell rest and activation

Nature. 2024 Dec 11. doi: 10.1038/s41586-024-08314-y. Online ahead of print.

Authors

Maya M Arce^{1

2

3}, Jennifer M Umhoefer^{1

2

3}, Nadia Arang⁴, Sivakanthan Kasinathan^{1

5}, Jacob W Freimer^{1

2

6}, Zachary Steinhart^{1

2}, Haolin Shen³, Minh T N Pham⁷, Mineto Ota^{1

2

6}, Anika Wadhera¹, Rama Dajani¹, Dmytro Dorovskyi^{1

2}, Yan Yi Chen^{1

2}, Qi Liu^{1

2}, Yuan Zhou^{4

8}, Danielle L Swaney^{4

8

9}, Kirsten Obernier^{4

8}, Brian R Shy^{1

10}, Julia Carnevale^{1

2

11

12}, Ansuman T Satpathy^{1

7

12}, Nevan J Krogan^{4

8

9

13}, Jonathan K Pritchard^{6

14}, Alexander Marson^{15

16

17

18

19

20

21}

Affiliations

¹ Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
² Department of Medicine, University of California, San Francisco, CA, USA.
³ Biomedical Sciences graduate program, University of California, San Francisco, CA, USA.
⁴ Quantitative Biosciences Institute (QBI), University of California, San Francisco, CA, USA.
⁵ Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
⁶ Department of Genetics, Stanford University, Stanford, CA, USA.
⁷ Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
⁸ Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.
⁹ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
¹⁰ Department of Laboratory Medicine, University of California, San Francisco, CA, USA.
¹¹ UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA.
¹² Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
¹³ Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.
¹⁴ Department of Biology, Stanford University, Stanford, CA, USA.
¹⁵ Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA. alex.marson@gladstone.ucsf.edu.
¹⁶ Department of Medicine, University of California, San Francisco, CA, USA. alex.marson@gladstone.ucsf.edu.
¹⁷ UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA. alex.marson@gladstone.ucsf.edu.
¹⁸ Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA. alex.marson@gladstone.ucsf.edu.
¹⁹ Innovative Genomics Institute, University of California-Berkeley, Berkeley, CA, USA. alex.marson@gladstone.ucsf.edu.
²⁰ Department of Microbiology and Immunology, University of California, San Francisco, CA, USA. alex.marson@gladstone.ucsf.edu.
²¹ Institute for Human Genetics, University of California, San Francisco, CA, USA. alex.marson@gladstone.ucsf.edu.

PMID: 39663454
DOI: 10.1038/s41586-024-08314-y

Abstract

The ability of cells to maintain distinct identities and respond to transient environmental signals requires tightly controlled regulation of gene networks^1-3. These dynamic regulatory circuits that respond to extracellular cues in primary human cells remain poorly defined. The need for context-dependent regulation is prominent in T cells, where distinct lineages must respond to diverse signals to mount effective immune responses and maintain homeostasis^4-8. Here we performed CRISPR screens in multiple primary human CD4⁺ T cell contexts to identify regulators that control expression of IL-2Rα, a canonical marker of T cell activation transiently expressed by pro-inflammatory effector T cells and constitutively expressed by anti-inflammatory regulatory T cells where it is required for fitness^9-11. Approximately 90% of identified regulators of IL-2Rα had effects that varied across cell types and/or stimulation states, including a subset that even had opposite effects across conditions. Using single-cell transcriptomics after pooled perturbation of context-specific screen hits, we characterized specific factors as regulators of overall rest or activation and constructed state-specific regulatory networks. MED12 - a component of the Mediator complex - serves as a dynamic orchestrator of key regulators, controlling expression of distinct sets of regulators in different T cell contexts. Immunoprecipitation-mass spectrometry revealed that MED12 interacts with the histone methylating COMPASS complex. MED12 was required for histone methylation and expression of genes encoding key context-specific regulators, including the rest maintenance factor KLF2 and the versatile regulator MYC. CRISPR ablation of MED12 blunted the cell-state transitions between rest and activation and protected from activation-induced cell death. Overall, this work leverages CRISPR screens performed across conditions to define dynamic gene circuits required to establish resting and activated T cell states.